Altas,
This does make sense to me, actually. I do know that some of the views basically only ask for 500 records when searching for a group to import, although I don't know if this is the case for the initial group import. If the issue is that you have thousands of groups, it could be that it just didn't make the list like your AD gurus are saying--I've heard of cases where a domain will have 20,000 groups, and even if all of them made it into the dropdown, it'd be nearly impossible to find the right one.
As far as editing the AD Query, I'm afraid that this is handled in compiled code, and can't be edited. However, if you know the name of the group you'd like to import, you could try using the 'Filter' option on the import screen. This should support AD wildcard syntax, so for your two groups you'd filter for FG_*